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I understand that this question has been asked before, but I am trying to measure the intensity of the fluorescence in certain regions of images using ImageJ. I came up with the below steps to measure the intensity. Though it appears correct, are we measuring intensity correctly using the following steps or are we wrongly measuring something else and believing that the value is the intensity?
Make the image a grayscale
Threshold the image to outline all the regions and click Apply
Open Analyze > Analyze particles. Click "add to manager"
Analyze > Analyze particles > Show > Bare Outlines. This will open a new image.
Open the color microscopy image. Then, Image > Overlay > From ROI Manager.
Image > Overlay > To ROI Manager.
In ROI Manager: press “measure.” (a Results window with individual data points will pop up)
Summarize the Results window
Record mean intensity data
Are we correctly measuring mean intensity data using the above steps?
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